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- PDB-1e5p: Crystal structure of aphrodisin, a sex pheromone from female hamster -

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Basic information

Entry
Database: PDB / ID: 1e5p
TitleCrystal structure of aphrodisin, a sex pheromone from female hamster
ComponentsAPHRODISIN
KeywordsLIPOCALIN / PHEROMONE / HAMSTER
Function / homology
Function and homology information


odorant binding / small molecule binding / extracellular space
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMESOCRICETUS AURATUS (golden hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å
AuthorsVincent, F. / Brown, K. / Spinelli, S. / Cambillau, C. / Tegoni, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of aphrodisin, a sex pheromone from female hamster.
Authors: Vincent, F. / Lobel, D. / Brown, K. / Spinelli, S. / Grote, P. / Breer, H. / Cambillau, C. / Tegoni, M.
History
DepositionJul 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / reflns / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _reflns.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APHRODISIN
B: APHRODISIN
C: APHRODISIN
D: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)69,5564
Polymers69,5564
Non-polymers00
Water12,665703
1
A: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)17,3891
Polymers17,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)17,3891
Polymers17,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)17,3891
Polymers17,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: APHRODISIN


Theoretical massNumber of molelcules
Total (without water)17,3891
Polymers17,3891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.050, 48.920, 123.547
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99583, -0.03603, 0.08386), (0.00504, 0.93907, 0.34368), (-0.09113, -0.34182, 0.93534)-2.18702, 10.94148, -14.25162
2given(-0.98626, 0.16046, 0.03936), (0.16233, 0.89681, 0.41155), (0.03074, 0.41229, -0.91053)-51.32672, -11.73474, 70.58553
3given(-0.99779, 0.03586, -0.05595), (0.03319, 0.9983, 0.04786), (0.05757, 0.04589, -0.99729)-43.31905, 22.33536, 61.29768

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Components

#1: Protein
APHRODISIN


Mass: 17389.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MESOCRICETUS AURATUS (golden hamster) / Gene: MESOCRICETUS AURATUS APHRODISIN GENE / Organ: VAGIN / Plasmid: PQE31 / Cellular location (production host): CYTOPLASM
Gene (production host): MESOCRICETUS AURATUS APHRODISIN GENE
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834DE3 / References: UniProt: P09465
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: APHRODISIN, SECRETED IN HAMSTER VAGINAL DISCHARGE, IT FUNCTIONS AS AN APHRODISIAC ...FUNCTION: APHRODISIN, SECRETED IN HAMSTER VAGINAL DISCHARGE, IT FUNCTIONS AS AN APHRODISIAC PHEROMONE, RELIABLY ELICITING COPULATORY BEHAVIOR FROM MALE HAMSTER. SIMILARITY: BELONGS TO THE LIPOCALIN FAMILY.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51 %
Crystal growMethod: vapor diffusion / pH: 3.8
Details: PEG 8K 28%, 150MM AS, 10MM NACL PH 3.8, [P]=2.65MG/NL
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Method: vapor diffusion / pH: 3.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
128 %PEG80001reservoir
2150 mMammonium sulfate1reservoir
3100 mMsodium citrate1reservoirpH3.8
42.65 mg/mlprotein1drop
52.5 M1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.978, 0.9795, 0.9324, 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 1999 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.97951
30.93241
40.9331
ReflectionResolution: 1.6→30 Å / Num. obs: 89441 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 23.77 Å2 / Rsym value: 0.099 / Net I/σ(I): 7.9
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.31 / % possible all: 94
Reflection
*PLUS
Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Rmerge(I) obs: 0.31

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: 1A3Y

1a3y


Resolution: 1.63→15 Å / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.098
Details: SEVERAL RESIDUES ARE IN ALTERNATE CONFORMATION, AND ARE PRECEEDED BY A AND B LIKE AMET, BMET. THE PROTEIN USED TO SOLVE THE STRUCTURE HAS BEEN SELENIATED SO THE METHIONINES IN THE PDB FILE ...Details: SEVERAL RESIDUES ARE IN ALTERNATE CONFORMATION, AND ARE PRECEEDED BY A AND B LIKE AMET, BMET. THE PROTEIN USED TO SOLVE THE STRUCTURE HAS BEEN SELENIATED SO THE METHIONINES IN THE PDB FILE ARE SELENOMETHIONIES (MSE) SOME OCCUPANCIES HAVE BEEN SET TO 0 OR LESS THAN 1 BECAUSE OF LACK OF DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2202 2.5 %RANDOM
Rwork0.194 ---
obs0.194 88875 96 %-
Refinement stepCycle: LAST / Resolution: 1.63→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 0 0 703 5456
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0290.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8292
X-RAY DIFFRACTIONp_mcangle_it2.5352.5
X-RAY DIFFRACTIONp_scbond_it2.8533
X-RAY DIFFRACTIONp_scangle_it3.964.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1870.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1220.3
X-RAY DIFFRACTIONp_planar_tor3.92
X-RAY DIFFRACTIONp_staggered_tor15.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.320
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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